BMP2 p.Pro93=
c.279C>T · rs539460039 · VCV1649042
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0637%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.5 | GERP -5.3 |
| Overall | ||
| CADD | 4.621 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0637%
South Asian · 58/91,014 alleles
Filtering AF
0.0506%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0458%
Overall
0.00385%
62/1,611,950 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0637% | 1,569 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,210 |
| Admixed American | 0.00167% | 59,958 |
| European (non-Finnish) | 8.48e-05% | 1,179,165 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BMP2
- Protein
- p.Pro93=
- Coding
- c.279C>T
- MANE Select
- NM_001200
- dbSNP
- rs539460039
- Type
- single nucleotide variant
- Location
- chr20:6770405 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.37 · 21 PDB
- Residue 93
- a UniProt-annotated variant site (in ssfsc1); the 'disordered' region
Similar variants
- BMP2 p.Pro93Leu Uncertain significance ★ ⚠ same residue
- BMP2 p.Arg154Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Cys329Ter Likely pathogenic ★★ same type
- BMP2 p.Gln89Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Glu229Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Ser92Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Ala103Thr Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bmp2-p-pro93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown